Showing NP-Card for L-Dihydroorotic acid (NP0000906)

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Record Information
Version2.0
Created at2006-08-12 19:12:38 UTC
Updated at2021-06-29 00:47:45 UTC
NP-MRD IDNP0000906
Secondary Accession NumbersNone
Natural Product Identification
Common NameL-Dihydroorotic acid
DescriptionL-Dihydroorotic acid, also known as (S)-4,5-dihydroorotate or dihydro-L-orotate, belongs to the class of organic compounds known as alpha amino acids and derivatives. These are amino acids in which the amino group is attached to the carbon atom immediately adjacent to the carboxylate group (alpha carbon), or a derivative thereof. 4,5-Dihydroorotic acid is a derivative of orotic acid which serves as an intermediate in pyrimidine biosynthesis. L-Dihydroorotic acid is a drug. L-Dihydroorotic acid exists in all living species, ranging from bacteria to humans. Within humans, L-dihydroorotic acid participates in a number of enzymatic reactions. In particular, L-dihydroorotic acid can be biosynthesized from ureidosuccinic acid; which is catalyzed by the enzyme cad protein. In addition, L-dihydroorotic acid and quinone can be converted into orotic acid through the action of the enzyme dihydroorotate dehydrogenase (quinone), mitochondrial. In humans, L-dihydroorotic acid is involved in the metabolic disorder called the beta-ureidopropionase deficiency pathway. Outside of the human body, L-dihydroorotic acid has been detected, but not quantified in several different foods, such as black chokeberries, vanilla, sweet basils, soy beans, and broad beans.
Structure
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MOL3D MOLSDF3D SDFPDB3D PDBSMILESInChI

MOL for NP0000906 (L-Dihydroorotic acid)

  Mrv1652309042000292D          

 11 11  0  0  1  0            999 V2000
    2.8579    0.0000    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.1434   -0.4125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.1434   -1.2375    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.4289    0.0000    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    0.7145   -0.4125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7145   -0.4125    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000    0.8250    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    0.7145    1.2375    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7145    2.0625    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.4289    0.8250    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0  0  0  0
  2  3  2  0  0  0  0
  4  2  1  6  0  0  0
  4  5  1  0  0  0  0
  5  6  1  0  0  0  0
  6  7  2  0  0  0  0
  6  8  1  0  0  0  0
  8  9  1  0  0  0  0
  9 10  2  0  0  0  0
  9 11  1  0  0  0  0
  4 11  1  0  0  0  0
M  END
Download

3D MOL for NP0000906 (L-Dihydroorotic acid)

HMDB0003349
     RDKit          3D
L-Dihydroorotic acid
 17 17  0  0  0  0  0  0  0  0999 V2000
   -2.6098   -0.6879    1.5485 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7442   -0.3138    0.7103 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5443   -1.1305    0.3609 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.5806   -0.0971    0.1672 C   0  0  1  0  0  0  0  0  0  0  0  0
    1.9006   -0.7090    0.1085 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.1712   -1.8674   -0.0305 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.9722    0.2145    0.2550 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.1530    0.5752   -1.0756 N   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0039    1.4080   -0.8477 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1595    2.5124   -1.4661 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9592    0.9313    0.0847 N   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7340   -1.5668   -0.6642 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2934   -1.8951    1.0593 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.5303    0.5551    1.0130 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.9115   -0.0350    0.4313 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.5929    0.5255   -1.9781 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.7642    1.5805    0.3234 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  2  0
  2  3  1  0
  3  4  1  0
  4  5  1  0
  5  6  2  0
  5  7  1  0
  4  8  1  0
  8  9  1  0
  9 10  2  0
  9 11  1  0
 11  2  1  0
  3 12  1  0
  3 13  1  0
  4 14  1  1
  7 15  1  0
  8 16  1  0
 11 17  1  0
M  END
Download

3D SDF for NP0000906 (L-Dihydroorotic acid)

  Mrv1652309042000292D          

 11 11  0  0  1  0            999 V2000
    2.8579    0.0000    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.1434   -0.4125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.1434   -1.2375    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.4289    0.0000    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    0.7145   -0.4125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7145   -0.4125    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000    0.8250    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    0.7145    1.2375    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7145    2.0625    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.4289    0.8250    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0  0  0  0
  2  3  2  0  0  0  0
  4  2  1  6  0  0  0
  4  5  1  0  0  0  0
  5  6  1  0  0  0  0
  6  7  2  0  0  0  0
  6  8  1  0  0  0  0
  8  9  1  0  0  0  0
  9 10  2  0  0  0  0
  9 11  1  0  0  0  0
  4 11  1  0  0  0  0
M  END
> <DATABASE_ID>
NP0000906

> <DATABASE_NAME>
NP-MRD

> <SMILES>
OC(=O)[C@@H]1CC(=O)NC(=O)N1

> <INCHI_IDENTIFIER>
InChI=1S/C5H6N2O4/c8-3-1-2(4(9)10)6-5(11)7-3/h2H,1H2,(H,9,10)(H2,6,7,8,11)/t2-/m0/s1

> <INCHI_KEY>
UFIVEPVSAGBUSI-REOHCLBHSA-N

> <FORMULA>
C5H6N2O4

> <MOLECULAR_WEIGHT>
158.1121

> <EXACT_MASS>
158.03275669

> <JCHEM_ACCEPTOR_COUNT>
4

> <JCHEM_ATOM_COUNT>
17

> <JCHEM_AVERAGE_POLARIZABILITY>
12.955416264529363

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
3

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
(4S)-2,6-dioxo-1,3-diazinane-4-carboxylic acid

> <ALOGPS_LOGP>
-1.70

> <JCHEM_LOGP>
-1.5232681353333333

> <ALOGPS_LOGS>
-1.10

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
1

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-1

> <JCHEM_PKA>
11.713668138573995

> <JCHEM_PKA_STRONGEST_ACIDIC>
3.2849203199118633

> <JCHEM_PKA_STRONGEST_BASIC>
-8.186843445720307

> <JCHEM_POLAR_SURFACE_AREA>
95.5

> <JCHEM_REFRACTIVITY>
31.575400000000005

> <JCHEM_ROTATABLE_BOND_COUNT>
1

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
1.27e+01 g/l

> <JCHEM_TRADITIONAL_IUPAC>
L-dihydroorotic acid

> <JCHEM_VEBER_RULE>
0

$$$$
Download

3D-SDF for NP0000906 (L-Dihydroorotic acid)

HMDB0003349
     RDKit          3D
L-Dihydroorotic acid
 17 17  0  0  0  0  0  0  0  0999 V2000
   -2.6098   -0.6879    1.5485 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7442   -0.3138    0.7103 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5443   -1.1305    0.3609 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.5806   -0.0971    0.1672 C   0  0  1  0  0  0  0  0  0  0  0  0
    1.9006   -0.7090    0.1085 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.1712   -1.8674   -0.0305 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.9722    0.2145    0.2550 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.1530    0.5752   -1.0756 N   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0039    1.4080   -0.8477 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1595    2.5124   -1.4661 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9592    0.9313    0.0847 N   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7340   -1.5668   -0.6642 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2934   -1.8951    1.0593 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.5303    0.5551    1.0130 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.9115   -0.0350    0.4313 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.5929    0.5255   -1.9781 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.7642    1.5805    0.3234 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  2  0
  2  3  1  0
  3  4  1  0
  4  5  1  0
  5  6  2  0
  5  7  1  0
  4  8  1  0
  8  9  1  0
  9 10  2  0
  9 11  1  0
 11  2  1  0
  3 12  1  0
  3 13  1  0
  4 14  1  1
  7 15  1  0
  8 16  1  0
 11 17  1  0
M  END
Download

PDB for NP0000906 (L-Dihydroorotic acid)

HEADER    PROTEIN                                 04-SEP-20   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   04-SEP-20         0                                  
HETATM    1  O   UNK     0       5.335   0.000   0.000  0.00  0.00           O+0
HETATM    2  C   UNK     0       4.001  -0.770   0.000  0.00  0.00           C+0
HETATM    3  O   UNK     0       4.001  -2.310   0.000  0.00  0.00           O+0
HETATM    4  C   UNK     0       2.667   0.000   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       1.334  -0.770   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM    7  O   UNK     0      -1.334  -0.770   0.000  0.00  0.00           O+0
HETATM    8  N   UNK     0       0.000   1.540   0.000  0.00  0.00           N+0
HETATM    9  C   UNK     0       1.334   2.310   0.000  0.00  0.00           C+0
HETATM   10  O   UNK     0       1.334   3.850   0.000  0.00  0.00           O+0
HETATM   11  N   UNK     0       2.667   1.540   0.000  0.00  0.00           N+0
CONECT    1    2                                                            
CONECT    2    1    3    4                                                  
CONECT    3    2                                                            
CONECT    4    2    5   11                                                  
CONECT    5    4    6                                                       
CONECT    6    5    7    8                                                  
CONECT    7    6                                                            
CONECT    8    6    9                                                       
CONECT    9    8   10   11                                                  
CONECT   10    9                                                            
CONECT   11    9    4                                                       
MASTER        0    0    0    0    0    0    0    0   11    0   22    0
END
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3D PDB for NP0000906 (L-Dihydroorotic acid)

COMPND    HMDB0003349
HETATM    1  O1  UNL     1      -2.610  -0.688   1.549  1.00  0.00           O  
HETATM    2  C1  UNL     1      -1.744  -0.314   0.710  1.00  0.00           C  
HETATM    3  C2  UNL     1      -0.544  -1.130   0.361  1.00  0.00           C  
HETATM    4  C3  UNL     1       0.581  -0.097   0.167  1.00  0.00           C  
HETATM    5  C4  UNL     1       1.901  -0.709   0.108  1.00  0.00           C  
HETATM    6  O2  UNL     1       2.171  -1.867  -0.031  1.00  0.00           O  
HETATM    7  O3  UNL     1       2.972   0.215   0.255  1.00  0.00           O  
HETATM    8  N1  UNL     1       0.153   0.575  -1.076  1.00  0.00           N  
HETATM    9  C5  UNL     1      -1.004   1.408  -0.848  1.00  0.00           C  
HETATM   10  O4  UNL     1      -1.159   2.512  -1.466  1.00  0.00           O  
HETATM   11  N2  UNL     1      -1.959   0.931   0.085  1.00  0.00           N  
HETATM   12  H1  UNL     1      -0.734  -1.567  -0.664  1.00  0.00           H  
HETATM   13  H2  UNL     1      -0.293  -1.895   1.059  1.00  0.00           H  
HETATM   14  H3  UNL     1       0.530   0.555   1.013  1.00  0.00           H  
HETATM   15  H4  UNL     1       3.912  -0.035   0.431  1.00  0.00           H  
HETATM   16  H5  UNL     1       0.593   0.525  -1.978  1.00  0.00           H  
HETATM   17  H6  UNL     1      -2.764   1.581   0.323  1.00  0.00           H  
CONECT    1    2    2
CONECT    2    3   11
CONECT    3    4   12   13
CONECT    4    5    8   14
CONECT    5    6    6    7
CONECT    7   15
CONECT    8    9   16
CONECT    9   10   10   11
CONECT   11   17
END
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SMILES for NP0000906 (L-Dihydroorotic acid)

OC(=O)[C@@H]1CC(=O)NC(=O)N1
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INCHI for NP0000906 (L-Dihydroorotic acid)

InChI=1S/C5H6N2O4/c8-3-1-2(4(9)10)6-5(11)7-3/h2H,1H2,(H,9,10)(H2,6,7,8,11)/t2-/m0/s1
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View in JSmol
Synonyms
ValueSource
(S)-4,5-Dihydroorotic acidChEBI
Dihydro-L-orotic acidChEBI
(S)-4,5-DihydroorotateKegg
L-DihydroorotateKegg
Dihydro-L-orotateGenerator
(S)-DihydroorotateHMDB
4,5-Dihydroorotic acid, (L)-isomerHMDB
5,6-DihydroorotateHMDB
4,5-Dihydroorotic acidHMDB
4,5-Dihydroorotic acid, (DL)-isomerHMDB
DihydroorotateHMDB
Hydroorotic acidHMDB
4,5-Dihydroorotic acid, (D)-isomerHMDB
Chemical FormulaC5H6N2O4
Average Mass158.1121 Da
Monoisotopic Mass158.03276 Da
IUPAC Name(4S)-2,6-dioxo-1,3-diazinane-4-carboxylic acid
Traditional NameL-dihydroorotic acid
CAS Registry Number5988-19-2
SMILES
OC(=O)[C@@H]1CC(=O)NC(=O)N1
InChI Identifier
InChI=1S/C5H6N2O4/c8-3-1-2(4(9)10)6-5(11)7-3/h2H,1H2,(H,9,10)(H2,6,7,8,11)/t2-/m0/s1
InChI KeyUFIVEPVSAGBUSI-REOHCLBHSA-N
Experimental Spectra
Spectrum TypeDescriptionDepositor EmailDepositor OrganizationDepositorDeposition DateView
1D NMR1H NMR Spectrum (1D, 600 MHz, H2O, experimental)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
2D NMR[1H, 13C]-HSQC NMR Spectrum (2D, 600 MHz, H2O, experimental)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
Predicted Spectra
Not Available
Chemical Shift Submissions
Not Available
Species
Species of Origin
Species Where Detected
Species NameSourceReference
Escherichia coliKNApSAcK Database
Chemical Taxonomy
Description Belongs to the class of organic compounds known as alpha amino acids and derivatives. These are amino acids in which the amino group is attached to the carbon atom immediately adjacent to the carboxylate group (alpha carbon), or a derivative thereof.
KingdomOrganic compounds
Super ClassOrganic acids and derivatives
ClassCarboxylic acids and derivatives
Sub ClassAmino acids, peptides, and analogues
Direct ParentAlpha amino acids and derivatives
Alternative Parents
Substituents
  • Alpha-amino acid or derivatives
  • N-acyl urea
  • Pyrimidone
  • Ureide
  • 1,3-diazinane
  • Pyrimidine
  • Dicarboximide
  • Urea
  • Carbonic acid derivative
  • Azacycle
  • Monocarboxylic acid or derivatives
  • Carboxylic acid
  • Organoheterocyclic compound
  • Hydrocarbon derivative
  • Organic oxide
  • Organooxygen compound
  • Organonitrogen compound
  • Organopnictogen compound
  • Organic oxygen compound
  • Carbonyl group
  • Organic nitrogen compound
  • Aliphatic heteromonocyclic compound
Molecular FrameworkAliphatic heteromonocyclic compounds
External Descriptors
Physical Properties
StateSolid
Experimental Properties
PropertyValueReference
Melting PointNot AvailableNot Available
Boiling PointNot AvailableNot Available
Water SolubilityNot AvailableNot Available
LogPNot AvailableNot Available
Predicted Properties
PropertyValueSource
Water Solubility12.7 g/LALOGPS
logP-1.7ALOGPS
logP-1.5ChemAxon
logS-1.1ALOGPS
pKa (Strongest Acidic)3.28ChemAxon
pKa (Strongest Basic)-8.2ChemAxon
Physiological Charge-1ChemAxon
Hydrogen Acceptor Count4ChemAxon
Hydrogen Donor Count3ChemAxon
Polar Surface Area95.5 ŲChemAxon
Rotatable Bond Count1ChemAxon
Refractivity31.58 m³·mol⁻¹ChemAxon
Polarizability12.96 ųChemAxon
Number of Rings1ChemAxon
BioavailabilityYesChemAxon
Rule of FiveYesChemAxon
Ghose FilterNoChemAxon
Veber's RuleNoChemAxon
MDDR-like RuleNoChemAxon
HMDB IDHMDB0003349
DrugBank IDDB02129
Phenol Explorer Compound IDNot Available
FoodDB IDFDB030169
KNApSAcK IDC00007302
Chemspider ID388355
KEGG Compound IDC00337
BioCyc IDDI-H-OROTATE
BiGG ID34662
Wikipedia Link4,5-Dihydroorotic acid
METLIN ID6899
PubChem Compound439216
PDB IDNot Available
ChEBI ID17025
Good Scents IDNot Available
References
General References
  1. Lee MH, Cowling RA, Sander EG, Pettigrew DW: Bovine liver dihydropyrimidine amidohydrolase: pH dependencies of inactivation by chelators and steady-state kinetic properties. Arch Biochem Biophys. 1986 Jul;248(1):368-78. doi: 10.1016/0003-9861(86)90433-9. [PubMed:3089167 ]
  2. Yin F, Ling Y, Martin J, Narayanaswamy R, McIntosh L, Li F, Liu G: Quantitation of uridine and L-dihydroorotic acid in human plasma by LC-MS/MS using a surrogate matrix approach. J Pharm Biomed Anal. 2021 Jan 5;192:113669. doi: 10.1016/j.jpba.2020.113669. Epub 2020 Oct 7. [PubMed:33120310 ]
  3. Zhang H, Zuo JJ, Dong SS, Lan Y, Wu CW, Mao GY, Zheng C: Identification of Potential Serum Metabolic Biomarkers of Diabetic Kidney Disease: A Widely Targeted Metabolomics Study. J Diabetes Res. 2020 Mar 2;2020:3049098. doi: 10.1155/2020/3049098. eCollection 2020. [PubMed:32190695 ]